Segger/map: cannot convert float infinity to integer

[chimerax-bug-report@…]

The following bug report has been submitted:
Platform:        Darwin-18.7.0-x86_64-i386-64bit
ChimeraX Version: 0.91 (2019-08-07)
Description
(Describe the actions that caused this problem to occur here)

Log:
UCSF ChimeraX version: 0.91 (2019-08-07)  
© 2016-2019 Regents of the University of California. All rights reserved.  
How to cite UCSF ChimeraX  

> open /Users/nimigeanlab/Desktop/emd_7484.map

Opened emd_7484.map, grid size 256,256,256, pixel 1.07, shown at level 0.0314,
step 1, values float32  

> toolshed show "Segment Map"

Segmenting emd_7484.map, density threshold 0.045993  
Showing emd_7484.seg - 0 regions, 0 surfaces  
Only showing 1000 of 2979 regions.  
Showing 1000 of 2979 region surfaces  
3993 watershed regions, grouped to 2979 regions  

> open "/Users/nimigeanlab/Documents/Philipp/1_data/reports/2019_NYC-
cryoEM/6cju_SthKcAMP_no ligands.pdb"

Summary of feedback from opening
/Users/nimigeanlab/Documents/Philipp/1_data/reports/2019_NYC-
cryoEM/6cju_SthKcAMP_no ligands.pdb  
---  
warning | CONECT record for nonexistent atom: 12413  
  
6cju_SthKcAMP_no ligands.pdb title:  
Structure of the STHK cyclic nucleotide-gated potassium channel In complex
with camp [more info...]  
  
Chain information for 6cju_SthKcAMP_no ligands.pdb #3  
---  
Chain | Description  
A B C D | STHK cyclic nucleotide-gated potassium channel  
  
Grouping with chains... making chain maps...  
Grouping with chains... making map for chain 1/4 of mol 1/1  

> molmap #3/A 0.000000 sigmaFactor 0.187 gridSpacing 0.000000 replace false

/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py:214: RuntimeWarning: divide by zero
encountered in double_scalars  
for a in (2,1,0)]  
Traceback (most recent call last):  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 3382, in GroupRegionsByChains  
mv = self._run_command ( cmd )  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/segger/fit_dialog.py", line 1629, in _run_command  
result = run ( self.session, command )  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/run.py", line 31, in run  
results = command.run(text, log=log)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/core/commands/cli.py", line 2655, in run  
result = ci.function(session, **kw_args)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 130, in molmap  
display_threshold, model_id, replace, show_dialog, name, session)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 145, in make_molecule_map  
transforms, name)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 193, in molecule_grid_data  
grid = bounding_grid(xyz, step, pad, transforms)  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in bounding_grid  
for a in (2,1,0)]  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in <listcomp>  
for a in (2,1,0)]  
OverflowError: cannot convert float infinity to integer  
  
OverflowError: cannot convert float infinity to integer  
  
File
"/Applications/ChimeraX_Daily.app/Contents/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-
packages/chimerax/map/molmap.py", line 214, in  
for a in (2,1,0)]  
  
See log for complete Python traceback.  
  




OpenGL version: 4.1 INTEL-12.10.12
OpenGL renderer: Intel(R) Iris(TM) Plus Graphics 655
OpenGL vendor: Intel Inc.

[Tom Goddard]

Fixed.

Segger fit to segments menu entry Group Regions by Chains was using 0 resolution in molmap -- never set the gui resolution value. Made code set resolution based on map grid spacing if value is 0 in gui.